/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/

// The example takes an image (say MRA image), computes the vesselness measure
// of the image using the HessianRecursiveGaussianImageFilter and the
// Hessian3DToVesselnessMeasureImageFilter. The goal is to detect bright tubular
// structures in the image.

#include "itkHessian3DToVesselnessMeasureImageFilter.h"
#include "itkHessianRecursiveGaussianImageFilter.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

int main( int argc, char *argv[] )
{
  if( argc < 3 )
    {
    std::cerr << "Usage: inputImage outputImage [sigma] [alpha_1] [alpha_2]" << std::endl;
    }

  constexpr unsigned int Dimension = 3;
  using InputPixelType = double;
  using OutputPixelType = float;

  using InputImageType = itk::Image< InputPixelType, Dimension >;
  using OutputImageType = itk::Image< OutputPixelType, Dimension >;

  using HessianFilterType = itk::HessianRecursiveGaussianImageFilter<InputImageType>;
  using VesselnessMeasureFilterType = itk::Hessian3DToVesselnessMeasureImageFilter<OutputPixelType>;
  using ReaderType = itk::ImageFileReader< InputImageType >;
  using WriterType = itk::ImageFileWriter< OutputImageType >;

  HessianFilterType::Pointer hessianFilter = HessianFilterType::New();
  VesselnessMeasureFilterType::Pointer vesselnessFilter =
                            VesselnessMeasureFilterType::New();

  ReaderType::Pointer   reader = ReaderType::New();
  WriterType::Pointer   writer = WriterType::New();

  reader->SetFileName( argv[1] );
  hessianFilter->SetInput( reader->GetOutput() );
  if( argc >= 4 )
    {
    hessianFilter->SetSigma( static_cast< double >(std::stod(argv[3])) );
    }
  vesselnessFilter->SetInput( hessianFilter->GetOutput() );
  writer->SetInput( vesselnessFilter->GetOutput() );
  writer->SetFileName( argv[2] );
  if( argc >= 5 )
    {
    vesselnessFilter->SetAlpha1( static_cast< double >(std::stod(argv[4])));
    }
  if( argc >= 6 )
    {
    vesselnessFilter->SetAlpha2( static_cast< double >(std::stod(argv[5])));
    }

  writer->Update();
  return EXIT_SUCCESS;
}
